An array is a collection of nucleic acid molecules of a chosen length, arranged in a spatially defined and physically addressable manner. Arrays of nucleic acid molecules are used in a variety of screening techniques such as diagnostics, scanning, sequencing and analysis of probes or target molecules, An array of probes such as nucleic acid molecules can be fabricated by depositing the preformed nucleic acid molecules on a substrate, or by forming nucleic acids using in situ synthesis techniques. In nucleic acid sequencing and analysis, there is a growing emphasis on the use of high density arrays of immobilized nucleic acid probes. The arrays can be used to assay for activity against a particular receptor, for screening in drug discovery, for sequencing, and as diagnostics.
Such arrays can be prepared by massive parallel schemes, e.g., using the selective photomask techniques described in U.S. Pat. No. 5,445,934. Arrays constructed in this manner are typically formed on a planar area of between about 4-100 mm.sup.2, and can have densities of up to several hundred thousand or more distinct array members/cm.sup.2. However, this method is expensive and requires sophisticated equipment. Further, this method requires photomask cells which are four times the nucleic acid probe length. Additionally, the photo-deprotection step is not as efficient as chemical deprotection, thus resulting in lower quality probes.
Conventional in situ synthesis using nanoliter drops can also be used to fabricate arrays, as described in, for example, U.S. Pat. No. 5,474,796 issued to Brennan. However, the number of arrays that can be produced in parallel using this technique is limited. Thus, fabrication of a large number of replicates of the same array is both labor- and time-intensive.
In order to avoid problems inherent in in situ synthesis techniques, polynucleotides can be synthesized prior to attachment to an appropriate substrate. U.S. Pat. Nos. 5,529,756 and 5,472,672, both issued to Brennan, describe an apparatus and a method for polymer synthesis. Preformed nucleic acid molecules can then be deposited on a substrate using several techniques, such as the method described in WO 95/35505 and U.S. Pat. No. 5,807,522. However, synthesis of such polynucleotides is laborious and expensive. Moreover, commercially available DNA synthesizers, such as the ABI 394 DNA Synthesizer, are limited to producing only 4 different oligonucleotides at a time.
Further, the transfer of nucleic acid molecule solutions from the original containers/chambers to the substrate requires a spatial translation from the original format to the final format. This translation is time-intensive and limits the number of parallel transfers possible. For example, WO 95/35505 and U.S. Pat. No. 5,807,522 describe a system to deposit presynthesized materials, wherein a pen-like capillary is used to transfer DNA or c-DNA solutions from a 96 well plate to glass microscope slides. The pen is dipped in the stock solution, and touched on the substrate to spot the liquid on the slide. However, this method has several disadvantages. For instance, the tips must be cleaned before contacting a different probe, and the tips dull easily. Further, the stock solutions are in a different spatial format from that of the actual array. This difference in formats limits the number of parallel transfers, making this process very time-consuming. For example, it would take approximately 50 hours to fabricate 100 arrays of 6000 different probes.
The above problems can be solved in part using robotics. However, current robotic technology can handle only a limited number of samples simultaneously.
Thus, there is a need for an improved apparatus and method to achieve more efficient fabrication of high density arrays, wherein the spatial format of the source of the nucleic acid molecules is similar to the array format, especially when the spatial format of the nucleic acid source is integral to the spatial formation of the deposition system and that of the final array.